The air is a hostile place for a microbe. Often dry, lacking in nutrients and filled with deadly ultraviolet radiation, the atmosphere would seem to be the last place a microbe would want to find itself. Yet, a new genetic census of some air samples from Austin and San Antonio, Tex., finds that as many as 2,000 different kinds of microbes may be present in the air we breathe on any given day.

Microbial ecologist Gary Andersen of Lawrence Berkeley National Laboratory and his colleagues collected air samples in the two Texas cities over a period of 17 weeks, starting in 2003. They then used a specially designed microarray--a small chip roughly the size of a quarter that carries probes to detect specific genetic information--to search for a gene involved in the making of a protein (16S) that is found in many microbes. "We designed a 500,000-probe array to identify up to about 9,000 different groups of bacterial and archaean organisms," Andersen explains. "It looks at the differences in the 16S sequence to identify a specific type of prokaryotic organism."

In the air samples, the researchers uncovered at least 1,800 different types of microbes, including those such as the diarrhea-causing Arcobacter and ulcer-inducing Heliobacter genera that can be dangerous to human health. Previous efforts to determine microbe counts in the atmosphere had relied on culturing the air to see what grew. "Over 90 percent you can't recover even though it was not only present but viable," Andersen notes. "It's just something about the physiological state it gets in; when it's not in rich media, it has a different physiology."

This puts the diversity of microbes in the air on par with the diversity of microbes in the soil, a fertile environment for such life-forms. In fact, there is a large crossover between the microbes in the air of a city and the microbes in its soil. The ecologists found that airborne microbes were broadly the same in Austin and San Antonio as well, and varied more depending on the weather than any other factor.

The most common microbes included those that thrive in hay fields and deteriorating exterior paint, according to the paper published online December 18 in Proceedings of the National Academy of Sciences USA. "We were surprised at how many different types of sequences we were seeing," Andersen adds. "Obscure phyla, like TM7, which have been seen in soil and gum tissue; hot springs type organisms; and microbes from sewage treatment plants."

The census provides a background for ongoing efforts by the U.S. Department of Homeland Security to monitor city air for potential bioterrorism attacks as well as fills in a gaping hole in the understanding of where microbes persist. For example, storms of Saharan dust--and their attendant microbes--have been linked to local meningitis outbreaks and tracked across the Pacific to coral deaths and an increase in childhood asthma in the Caribbean. "It's important to do a microbial census to see what's in the air we breathe. I believe it's going to change as the climate changes," Andersen says. "We may see very different populations of microbes in the air and that may have some health implications."

The air is now being tested in at least 30 U.S. cities and Andersen hopes the effort will be broadened. "How is it in the middle of the oceans?" he asks. "Is it just what's coming up from the sea's surface or is it a long-range dispersal of organisms?" Whatever the case, fresh, clean, bacteria-free air is rarer than previously thought.

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